Devices, systems, and methods for avoiding collisions between a manipulator arm and an outer patient surface by moving the manipulator within a null-space. In response to a determination that distance between an avoidance geometry and obstacle surface, corresponding to a manipulator-to-patient distance is less than desired, the system calculates movement of one or more joints or links of the manipulator within a null-space of the Jacobian to increase this distance. The joints are driven according to the reconfiguration command and calculated movement so as to maintain a desired state of the end effector. In one aspect, the joints are also driven according to a calculated end effector displacing movement within a null-perpendicular-space of the Jacobian to effect a desired movement of the end effector or remote center while concurrently avoiding arm-to-patient collisions by moving the joints within the null-space.